Can I still apply a stepwise approach to reference run selection and alignment?
Loading your LC-MS runs, selecting a reference and applying alignment step-by step is still possible in Progenesis LC-MS v4.1. This is useful when you need to set up proof-of-concept or pilot experiments and explore the quality of your runs that the LC-MS system produces.
The ion intensity maps you see as you load each run provide a visual feedback to help optimise settings while the system is in operation and improve the quality of LC-MS runs for reliable results.
Manually selecting the reference run and applying alignment also guide you to which runs you can use for more automated analysis of significantly higher numbers of replicates in the future. You can reduce automated processing time by selecting a single run or a limited set of runs, which routinely produce the best alignment scores, for the software to choose a reference from.